Lectures

You can download the lectures here (in PDF format). I will try to upload lectures prior to their corresponding classes.

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  Introduction
  tl;dr: Introduction to the class and some basic bio.
  

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  Sequencing Technologies
  tl;dr: Brief intro to the basics of short and long read sequencing.
  

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  Introduction to Alignment, Mapping and Indexing
  tl;dr: Basic alignment & the utility of exact matching.
  

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  The Suffix Array and Its Construction
  tl;dr: Why the SA is awesome.
  

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  The FM index and it's use in short-read alignment
  tl;dr: Why the FM-index is also very cool.
  

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  The FMD and Graph FM Indices
  tl;dr: Indices related to the FM-index.
  

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  The Practical Application of Full-text Indices
  tl;dr: What different aligners enable, in practice
  

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  Primitives for succinct data structures
  tl;dr: Succinct data structures are wicked cool!
  

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  K-mer counting, cardinality estimation, AMQs and MPHFs (oh my!)
  tl;dr: Dealing with discrete keys efficiently
  

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  Large-scale sequence search, part 1
  tl;dr: Searching the sea of sequencing data
  

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  Efficient de Bruijn graph representation
  tl;dr: Being clever about graph representation
  

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  Efficient colored de Bruijn graph representation
  tl;dr: Being clever about color representation
  

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  Efficient compacted colored de Bruijn graph construction
  tl;dr: TwoPaCo
  

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  Efficient indexing of the (compacted) colored de Bruijn graph
  tl;dr: using the (c)cdbg as an index
  

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  Analysis of transcriptomes with RNA-seq
  tl;dr: basics and ref-guided assembly
  

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  Analysis of transcriptomes with RNA-seq (II)
  tl;dr: more RNA-seq analysis
  

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